GTR Test Accession:
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GTR000210160.4
Last updated in GTR: 2024-02-07
View version history
GTR000210160.4, last updated: 2024-02-07
GTR000210160.3, last updated: 2023-02-08
GTR000210160.2, last updated: 2016-02-17
GTR000210160.1, last updated: 2013-05-03
Last annual review date for the lab: 2024-02-07
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic; ...
Conditions (5):
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Genes (1):
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TP53 (17p13.1)
Methods (3):
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Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Not provided
Clinical validity:
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It is estimated that 80% of families with LFS will …
Clinical utility:
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Establish or confirm diagnosis;
Predictive risk information for patient and/or family members
Ordering Information
Offered by:
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Test short name:
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p53
Specimen Source:
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- Amniocytes
- Cell culture
- Isolated DNA
- Peripheral (whole) blood
- White blood cell prep
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Licensed Physician
Test Order Code:
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Li Fraumeni Syndrome (p53)
LOINC codes:
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Lab contact:
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Contact Policy:
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Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order:
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Please complete the requisition found on our website and sign and submit with the appropriate sample. See shipping instructions for further details
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Confirmation of research findings
Test additional service:
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Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Custom mutation-specific/Carrier testing
Test development:
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Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required:
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Decline to answer
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Recommended fields not provided:
Test strategy
Conditions
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Total conditions: 5
Condition/Phenotype | Identifier |
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Test Targets
Genes
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Total genes: 1
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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Methodology
Total methods: 3
Method Category
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Test method
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Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina MiSeq/NextSeq
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Applied Biosystems 3730 capillary sequencing instrument
Illumina MiSeq/NextSeq
Illumina MiSeq/NextSeq
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic;
Predictive;
Risk Assessment
Clinical validity:
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It is estimated that 80% of families with LFS will harbour an identifiable TP53 mutation.
View citations (1)
- Li-fraumeni syndrome. Malkin D, et al. Genes Cancer. 2011;2(4):475-84. doi:10.1177/1947601911413466. PMID: 21779515.
Clinical utility:
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Establish or confirm diagnosis
Predictive risk information for patient and/or family members
Predictive risk information for patient and/or family members
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Novel variations are interrogated using a series of tools. Literature reviews and a search of relevant databases and dbSNP is pursued. This is followed by evaluation using web based insilco analysis including, but not restricted to SIFT, Polyphen2, AlignGVGD, SNPs&GO and ASSEDA(splice). If the pathogenicity is still indeterminate (ACMG group … View more
Novel variations are interrogated using a series of tools. Literature reviews and a search of relevant databases and dbSNP is pursued. This is followed by evaluation using web based insilco analysis including, but not restricted to SIFT, Polyphen2, AlignGVGD, SNPs&GO and ASSEDA(splice). If the pathogenicity is still indeterminate (ACMG group … View more
Will the lab re-contact the ordering physician if variant interpretation changes?
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Not provided.
Not provided.
Recommended fields not provided:
Target population,
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Will the lab re-contact the ordering physician if variant interpretation changes?,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations in a single assay that …
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View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Test Confirmation:
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All positive results and known familial mutations are confirmed by a second independent method
Test Comments:
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Direct sequence of all coding exons
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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The LHSC NGS protocol is predicted to detect in excess of 99% of mutations present within the genes listed. Mutation detection rates in the patient are dependent on the clinical presentation including age of onset, specific diagnostic features, and family history.
View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Proficiency testing (PT):
Is proficiency testing performed for this test?
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No
No
VUS:
Software used to interpret novel variations
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ALAMUT, integrating other programs (Polyphen-2, Mutation Taster, Alignment, ExPASy, BLAST)
Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.
ALAMUT, integrating other programs (Polyphen-2, Mutation Taster, Alignment, ExPASy, BLAST)
Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.
Recommended fields not provided:
Assay limitations,
Description of internal test validation method,
PT Provider,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
Not Applicable
Additional Information
Suggested reading:
Clinical resources:
Molecular resources:
Practice guidelines:
Consumer resources:
IMPORTANT NOTE:
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NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice.
Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.